Hello,<br><br>I am attempting to increase the density using NPT. As I increase the pressure to compress the system after some steps simulation crashes. I thought maybe its becasue I am compressing too fast but even when I take a stepwise approach to compress gradually the same error comes up. The density at the point of crash is about 30 SI while I need 650 which is the actual density. Topology file is generated successfully and also I did EM before MD.<br>
<br>Initial box size is 30 nm. As suggested in the link below I reduced the size to 20 nm (there are 2500 atoms in the system ) but the same error appears.<br><a href="http://lists.gromacs.org/pipermail/gmx-users/2009-April/041488.html">http://lists.gromacs.org/pipermail/gmx-users/2009-April/041488.html</a><br>
<br>I also tried less -np from 7 to 4 but no success.<br><br>
Can you please tell me what this exclamation mark mean which I get at times in parallel trials.(vol 0.99 !)<br><br>Thank you for your time.<br><br><br>vol 0.99! imb F 47% step 168000, will finish Fri Mar 4 00:51:29 2011<br>
vol 0.99! imb F 42% step 168100, will finish Fri Mar 4 00:51:26 2011<br>vol 0.99! imb F 44% step 168200, will finish Fri Mar 4 00:51:30 2011<br>vol 1.00! imb F 46% step 168300, will finish Fri Mar 4 00:51:27 2011<br>vol 1.00! imb F 48% step 168400, will finish Fri Mar 4 00:51:25 2011<br>
<br>-------------------------------------------------------<br>Program mdrun_mpi, VERSION 4.0.7<br>Source code file: domdec.c, line: 2592<br><br>Fatal error:<br>The X-size of the box (5.499734) times the triclinic skew factor (1.000000) is smaller than the number of DD cells (7) times the smallest allowed cell size (0.785678)<br>
========================================<br><br>Program mdrun_mpi, VERSION 4.0.7<br>Source code file: domdec.c, line: 2592<br><br>Fatal error:<br>The X-size of the box (4.999741) times the triclinic skew factor (1.000000) is smaller than the number of DD cells (4) times the smallest allowed cell size (1.250000)<br>
<br>====================================<br>pbc = xyz <br><br> <br>; Run control <br>integrator = md <br>
dt = 0.002 <br>nsteps = 1000000 ;5000 <br>nstcomm = 100 <br><br>; Output control<br>nstenergy = 100 <br>
nstxout = 100 <br>nstvout = 0<br>nstfout = 0<br>nstlog = 1000 <br>nstxtcout = 1000 <br><br>; Neighbor searching<br>
nstlist = 10 <br>ns_type = grid <br><br>; Electrostatics/VdW <br>coulombtype = PME <br>vdw-type = Shift <br>
rcoulomb-switch = 0 <br>rvdw-switch = 0.9 ;0 <br><br>; Cut-offs<br>rlist = 1.25 <br>rcoulomb = 1.25 ;1.1 <br>rvdw = 1.0 <br>
<br>; PME parameters<br>fourierspacing = 0.3 <br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4 <br>ewald_rtol = 1e-5<br>
optimize_fft = yes<br><br>; Temperature coupling <br>Tcoupl = v-rescale <br>tc-grps = System ;HEX <br>tau_t = 0.1 ;0.1 <br>
ref_t = 400 ;300 <br><br>; Pressure coupling<br>Pcoupl = Parrinello-Rahman <br>Pcoupltype = isotropic <br>tau_p = 1 1 ;0.5 <br>
compressibility = 4.5e-5 4.5e-5 <br>ref_p = 8 8 <br><br>; Velocity generation <br>gen_vel = yes <br>gen_temp = 300.0 <br>
gen_seed = 173529 <br><br>; Bonds<br>constraints = all-bonds <br>constraint-algorithm = lincs<br>
<br><br><br><br>